Subject: Bioinformatics Table of Contents for 15 January 2019 ------=_Part_711842760.1547571054149 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_711842760.1547571054149 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 35 Issue 2
 
15 January 2019
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Using tree-based methods for detection of gene'gene interactions in the presence of a polygenic signal: simulation study with application to educational attainment in the Generation Scotland Cohort Study border= 
 
Joeri J Meijsen ; Alexandros Rammos; Archie Campbell; Caroline Hayward; David J Porteous ...
 
 
ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation border= 
 
Malene Juul ; Tobias Madsen; Qianyun Guo; Johanna Bertl; Asger Hobolth ...
 
 
Statistical tests for detecting variance effects in quantitative trait studies border=  
 
Bianca Dumitrascu; Gregory Darnell; Julien Ayroles ; Barbara E Engelhardt
 
 
Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points border= 
 
Chris-André Leimeister ; Thomas Dencker; Burkhard Morgenstern
 
 
Metagenomic binning through low-density hashing border= 
 
Yunan Luo; Yun William Yu; Jianyang Zeng ; Bonnie Berger; Jian Peng
 
 
 
SEQUENCE ANALYSIS
 
 
 
CoMSA: compression of protein multiple sequence alignment files 
 
Sebastian Deorowicz; Joanna Walczyszyn; Agnieszka Debudaj-Grabysz
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Computational analysis of kinase inhibitor selectivity using structural knowledge 
 
Yu-Chen Lo; Tianyun Liu; Kari M Morrissey; Satoko Kakiuchi-Kiyota ; Adam R Johnson ...
 
 
LigVoxel: inpainting binding pockets using 3D-convolutional neural networks 
 
Miha Skalic; Alejandro Varela-Rial; José Jiménez; Gerard Martínez-Rosell ; Gianni De Fabritiis
 
 
 
GENE EXPRESSION
 
 
 
Xolik: finding cross-linked peptides with maximum paired scores in linear time 
 
Jiaan Dai; Wei Jiang; Fengchao Yu; Weichuan Yu
 
 
Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios 
 
Emmanuel Curis; Cindie Courtin; Pierre Alexis Geoffroy; Jean-Louis Laplanche ; Bruno Saubaméa ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Flux tope analysis: studying the coordination of reaction directions in metabolic networks border= 
 
Matthias P Gerstl; Stefan Müller; Georg Regensburger; Jürgen Zanghellini
 
 
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results border=  
 
Clément Frainay; Sandrine Aros; Maxime Chazalviel ; Thomas Garcia; Florence Vinson ...
 
 
Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models border= 
 
Olivia Eriksson ; Alexandra Jauhiainen; Sara Maad Sasane; Andrei Kramer; Anu G Nair ...
 
 
 
DATA AND TEXT MINING
 
 
 
Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics 
 
Piotr Klukowski; Mario Schubert
 
 
Reverse-engineering flow-cytometry gating strategies for phenotypic labelling and high-performance cell sorting 
 
Etienne Becht; Yannick Simoni; Elaine Coustan-Smith; Maximilien Evrard ; Yang Cheng ...
 
 
Compound'protein interaction prediction with end-to-end learning of neural networks for graphs and sequences 
 
Masashi Tsubaki; Kentaro Tomii; Jun Sese
 
 
 
BIOIMAGE INFORMATICS
 
 
 
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction border= 
 
Renmin Han ; Xiaohua Wan; Lun Li; Albert Lawrence; Peng Yang ...
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
GeneSpy, a user-friendly and flexible genomic context visualizer 
 
Pierre Simon Garcia; Frédéric Jauffrit; Christophe Grangeasse; Céline Brochier-Armanet
 
 
 
SEQUENCE ANALYSIS
 
 
 
3DPatch: fast 3D structure visualization with residue conservation border=  
 
David Jakubec; Jiří Vondrášek; Robert D Finn
 
 
PingPongPro: a tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data 
 
Sebastian Uhrig; Holger Klein
 
 
Crumble: reference free lossy compression of sequence quality values border=  
 
James K Bonfield; Shane A McCarthy; Richard Durbin
 
 
 
GENE EXPRESSION
 
 
 
TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts border= 
 
Dana Wyman; Ali Mortazavi
 
 
BrainImageR: spatiotemporal gene set analysis referencing the human brain 
 
Sara B Linker; Jonathan Y Hsu; Adela Pfaff; Debha Amatya ; Shu-Meng Ko ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
SLIDE ' a web-based tool for interactive visualization of large-scale ' omics data border= 
 
Soumita Ghosh; Abhik Datta ; Kaisen Tan; Hyungwon Choi
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
SATurn: a modular bioinformatics framework for the design of robust maintainable web-based and standalone applications border= 
 
David R Damerell ; Claire Strain-Damerell; Sefa Garsot; Stephen P Joyce; Paul Barrett ...
 
 
 
REVIEW
 
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Exosomal lncRNAs and cancer: connecting the missing links 
 
Hojjat Naderi-Meshkin; Xin Lai; Raheleh Amirkhah; Julio Vera ; John E J Rasko ...
 
 
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